Molecular Playground/Caspase-7 Dynamics - Revision history

Maureen E. Hill at 20:02, 3 December 2013

2013-12-03T20:02:29Z

←Older revision		Revision as of 20:02, 3 December 2013
Line 1:		Line 1:
-	Caspases are a family of [[CBI Molecules]] being studied ~~in the [http://www.chem.umass.edu/~jhardy/ Hardy Lab]~~ in the <span class="plainlinks">[http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program]</span> at UMass Amherst and on display at the <span class="plainlinks">[http://www.molecularplayground.org/ Molecular Playground]</span>.	+	Caspases are a family of [[CBI Molecules]] being studied in the <span class="plainlinks">[http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program]</span> at UMass Amherst and on display at the <span class="plainlinks">[http://www.molecularplayground.org/ Molecular Playground]</span>.

-	== ~~Executioner~~ Caspase-7 ==	+	=== Caspase-7 as studied in <span class="plainlinks">[http://www.chem.umass.edu/~jhardy/ the Hardy Lab] </span>===
-	<~~StructureSection~~ load='~~1f1j~~' size='~~350~~' ~~side~~='right' caption='~~Structure of~~ caspase-7~~(PDB entry [[1f1j]]) bound to tetra peptide substrate mimic DEVD-CHO' scene=~~'56/~~566502/Caspase_7_load_scene/1'~~>	+	<applet load='Caspmorph.pdb' size='300' frame='true' scene='Molecular_Playground/Caspase_Dynamics/Morph2/2' align='right' caption='Conformational Dynamics between active and allosterically inhibited caspase-7 elucidate the mechanism of allostery in this important class of cysteine proteases.' />

-	~~== Background ==~~	+	Conformational dynamics in Caspase-7 are mediated by an 'Allosteric Toggle' mechanism in which binding of allosteric inhibitor DICA to CYS 290 pushes TYR 223 into 'up' conformation forcing ARG 187 'out' into a form that is physically incompatible with substrate binding.

-	~~Caspases are cysteine-aspartate proteases that are responsible for~~ the ~~execution of apoptosis, also known as programmed cell death. Dysregulation of apoptosis has been linked to neurodegenerative disorders, including Alzheimer's~~ and ~~Huntington's~~, ~~as well as inflammatory diseases~~ and ~~cancer~~.	+	The cleaved termini of the large and small subunits which form the active site loop bundle become highly ordered in active conformation, and highly disordered in allosterically inhibited form (so much so that they cannot be resolved crystallographically).

-	~~The apoptotic caspases consist~~ of ~~two distinct classes: the initiators (caspase -2, -8, -9, and -10) and the executioners (caspase -3, -6, and~~ -7). All caspases are synthesized as catalytically inactive zymogens that must undergo proteolytic cleavage to be activated during apoptosis. Initiator caspases are activated by upstream cellular events, which in turn cleave at distinct internal aspartate residues in the executioner caspases to remove the prodomain and separate the large and small subunits. The executioner caspases then cleave a wide range of targets within the cell that ultimately leads to cellular suicide.	+	=== Forms of Caspase-7 ===

-	== Caspase-7 ~~Structure ==~~	+	*<scene name='Molecular_Playground/Caspase_Dynamics/1f1j/2'>Caspase-7 bound to suicide inhibitor/substrate mimic DEVD-CHO</scene>, trapping protein in active/substrate bound conformation.
-	~~[[Image:CASP7cleavagesites.jpg \| thumb\| Cleavage sites of caspase~~-~~7]]~~	+	*<scene name='Molecular_Playground/Caspase_Dynamics/1shj-234234/1'>Caspase-7 bound to allosteric inhibitor DICA through CYS290</scene> trapping protein in a form incompatible with substrate binding.
-	~~Caspases are crystallized as homodimers. As previously stated~~, ~~the caspases undergo proteolytic cleavage by the initiator caspases to assume their~~ active ~~conformations. Some caspases undergo more cleavage than others~~. Caspase-7 ~~has three major cleavage sites: D23, D198 and D207~~. ~~D23 processing removes the prodomain from the large subunit, whereas D198~~ and ~~D207 are the major cleavage sites for processing and removal~~ of ~~the inter-subunit linker.~~ Caspase-7 ~~has one minor cleavage site also located within the intersubunit linker at D192~~.	+	*<scene name='Molecular_Playground/Caspase_Dynamics/Morph2/2'>Conformational change between substrate bound and substrate incompatible forms</scene> of Caspase-7.

		+	=== Molecular Playground banner for Caspase-7 ===

-	~~The <scene name=~~'~~56/566502/Active_site_conformation/1~~'~~>active site</scene> is made up of four flexible loops which include L2, L3 and L4 from one half of the dimer that interact with L2~~' ~~from the opposite half of the dimer. In the <scene name=~~'~~56/566502/Procaspase_zymogen/1~~'~~>procaspase-7 zymogen</scene>, the loops are disordered, which prevents substrate binding. Upon cleavage at the intersubunit linker, the~~ active~~-site loop bundle becomes partially ordered, whereas L2' stays in the inactive, down conformation. At this point,~~ caspase-7 ~~may bind either substrate or allosteric inhibitors. <scene name='56/566502/Active_site_substrate_color/1'>Caspase-7 bound to suicide inhibitor/substrate mimc DEVD-CHO</scene> traps~~ the protein an active/substrate bound conformation. Substrate binding forces a conformational change moving L2' upward; this creates a foundation beneath the L2 bundle stabilizing the active complex. Mutagenesis performed within this region of ~~the protein has a significant impact on the ability of the protein to process its substrates. Ultimately,~~ this ~~confirms the importance~~ of ~~L2' stabilizing the active site loop bundle~~.	+	'''Molecular Playground banner:''' Conformational Dynamics between active and allosterically inhibited caspase-7 elucidate the mechanism of allostery in this important class of cysteine proteases.

		+	==3D structures of caspase==

-	~~== Allosteric Inhibition of~~ Caspase~~-7 ==~~	+	[[Caspase]]
-	It has been shown that caspases -3 and -7 can be inhibited at a site other than the active site by allosteric inhibitors, such as 5-Fluoro-1H-indole-2-carboxylic acid (2-mercapto-ethyl)-amide ('''FICA''') or 2-(2,4-Dichlorophenoxy)-N-(2-mercapto-ethyl)-acetamide ('''DICA'''), at the dimer-interface cavity. These inhibitors inactivate the enzyme on three different levels by: a) locking the L2' in a down conformation preventing it from ordering the active site loop bundles, b) rearranging the active site dyad H144 and C186, thereby affecting the ability to perform its chemistry, c) a conformational shift of residue R187, blocking substrate binding.	+

-	~~<scene name~~='56/566502/Dica_bound_caspase_7/2'>Caspase-7 bound to allosteric inhibitor DICA</scene> at the dimer interface. The mechanism of allosteric inhibition of DICA starts with binding to C290 within the dimer interface, this displaces Y223. The movement of tyrosine from the partially active state of the enzyme forces R187 into a position that both physically blocks substrate binding, as well as, move the active site cysteine 186. The resulting conformational changes inactivate the enzyme, making it unable to process substrate.	+	==Additional Resources==
-		+	For additional information, see: [[Cancer]]
-		+	<br />
-	=~~= Caspase-7 Dynamics~~ ==	+
-		+
-		+
-	~~Observed here is the~~ <~~scene name='Molecular_Playground~~/~~Caspase_Dynamics/Morph2/2'~~>conformational change between substrate bound and substrate incompatible forms</scene> of Caspase-7. These dynamics show the dramatic conformational change of the cleaved semi-ordered protease upon binding to the substrate mimic DEVD-CHO. Substrate binding triggers rearrangement of the partially ordered loop bundles and the L2' loop. The newly assumed state stabilizes the protein.	+
-		+
-		+
-	~~== References ==~~	+
-		+
-	~~Hardy, J. A., J. Lam, et al. (2004). "Discovery of an allosteric site in the caspases." Proc Natl Acad Sci U S A 101(34): 12461-12466.~~	+
-		+
-	~~Witkowski, W. a, & Hardy, J. a. (2009). L2’ loop is critical for caspase-7 active site formation. Protein science : a publication of the Protein Society, 18(7), 1459–68. doi:10.1002/pro.151~~	+
-		+
-	~~Witkowski, W. a, & Hardy, J. a. (2011). A designed redox-controlled caspase. Protein science : a publication of the Protein Society, 20(8), 1421–31. doi:10.1002/pro.673~~	+

Maureen E. Hill at 19:55, 3 December 2013

2013-12-03T19:55:55Z

←Older revision		Revision as of 19:55, 3 December 2013
Line 1:		Line 1:
-	Caspases are a family of [[CBI Molecules]] being studied in the <span class="plainlinks">[http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program]</span> at UMass Amherst and on display at the <span class="plainlinks">[http://www.molecularplayground.org/ Molecular Playground]</span>.	+	Caspases are a family of [[CBI Molecules]] being studied in the [http://www.chem.umass.edu/~jhardy/ Hardy Lab] in the <span class="plainlinks">[http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program]</span> at UMass Amherst and on display at the <span class="plainlinks">[http://www.molecularplayground.org/ Molecular Playground]</span>.

-	=== Caspase-7 ~~as studied in <span class="plainlinks">[http://www.chem.umass.edu/~jhardy/ the Hardy Lab] </span>=~~==	+	== Executioner Caspase-7 ==
-	<~~applet~~ load='~~Caspmorph.pdb~~' size='~~300~~' ~~frame='true' scene='Molecular_Playground/Caspase_Dynamics/Morph2/2' align~~='right' caption='~~Conformational Dynamics between active and allosterically inhibited~~ caspase-7 ~~elucidate the mechanism of allostery in this important class of cysteine proteases.~~' />	+	<StructureSection load='1f1j' size='350' side='right' caption='Structure of caspase-7(PDB entry [[1f1j]]) bound to tetra peptide substrate mimic DEVD-CHO' scene='56/566502/Caspase_7_load_scene/1'>

-	Conformational dynamics in Caspase-7 are mediated by an 'Allosteric Toggle' mechanism in which binding of allosteric inhibitor DICA to CYS 290 pushes TYR 223 into 'up' conformation forcing ARG 187 'out' into a form that is physically incompatible with substrate binding.	+	== Background ==

-	~~The cleaved termini of~~ the ~~large~~ and ~~small subunits which form the active site loop bundle become highly ordered in active conformation~~, and ~~highly disordered in allosterically inhibited form (so much so that they cannot be resolved crystallographically)~~.	+	Caspases are cysteine-aspartate proteases that are responsible for the execution of apoptosis, also known as programmed cell death. Dysregulation of apoptosis has been linked to neurodegenerative disorders, including Alzheimer's and Huntington's, as well as inflammatory diseases and cancer.

-	~~=== Forms~~ of ~~Caspase~~-7 ~~===~~	+	The apoptotic caspases consist of two distinct classes: the initiators (caspase -2, -8, -9, and -10) and the executioners (caspase -3, -6, and -7). All caspases are synthesized as catalytically inactive zymogens that must undergo proteolytic cleavage to be activated during apoptosis. Initiator caspases are activated by upstream cellular events, which in turn cleave at distinct internal aspartate residues in the executioner caspases to remove the prodomain and separate the large and small subunits. The executioner caspases then cleave a wide range of targets within the cell that ultimately leads to cellular suicide.

-	*<scene name=~~'Molecular_Playground/Caspase_Dynamics/1f1j/2'>~~Caspase-7 ~~bound to suicide inhibitor/substrate mimic DEVD~~-~~CHO</scene>~~, ~~trapping protein in~~ active~~/substrate bound conformation~~.	+	== Caspase-7 Structure ==
-	*<scene name='Molecular_Playground/Caspase_Dynamics/1shj-234234/1'>Caspase-7 ~~bound to allosteric inhibitor DICA through CYS290</scene> trapping protein in a form incompatible with substrate binding~~.	+	[[Image:CASP7cleavagesites.jpg \| thumb\| Cleavage sites of caspase-7]]
-	*<scene name='Molecular_Playground/Caspase_Dynamics/Morph2/2'>Conformational change between substrate bound and ~~substrate incompatible forms</scene>~~ of Caspase-7.	+	Caspases are crystallized as homodimers. As previously stated, the caspases undergo proteolytic cleavage by the initiator caspases to assume their active conformations. Some caspases undergo more cleavage than others. Caspase-7 has three major cleavage sites: D23, D198 and D207. D23 processing removes the prodomain from the large subunit, whereas D198 and D207 are the major cleavage sites for processing and removal of the inter-subunit linker. Caspase-7 has one minor cleavage site also located within the intersubunit linker at D192.

-	=== Molecular Playground banner for Caspase-7 ===

-	'''~~Molecular Playground banner:~~''~~' Conformational Dynamics between~~ active ~~and allosterically inhibited~~ caspase-7 ~~elucidate~~ the ~~mechanism~~ of ~~allostery in~~ this ~~important class~~ of ~~cysteine proteases~~.	+	The <scene name='56/566502/Active_site_conformation/1'>active site</scene> is made up of four flexible loops which include L2, L3 and L4 from one half of the dimer that interact with L2' from the opposite half of the dimer. In the <scene name='56/566502/Procaspase_zymogen/1'>procaspase-7 zymogen</scene>, the loops are disordered, which prevents substrate binding. Upon cleavage at the intersubunit linker, the active-site loop bundle becomes partially ordered, whereas L2' stays in the inactive, down conformation. At this point, caspase-7 may bind either substrate or allosteric inhibitors. <scene name='56/566502/Active_site_substrate_color/1'>Caspase-7 bound to suicide inhibitor/substrate mimc DEVD-CHO</scene> traps the protein an active/substrate bound conformation. Substrate binding forces a conformational change moving L2' upward; this creates a foundation beneath the L2 bundle stabilizing the active complex. Mutagenesis performed within this region of the protein has a significant impact on the ability of the protein to process its substrates. Ultimately, this confirms the importance of L2' stabilizing the active site loop bundle.

-	==3D structures of caspase==

-	[[Caspase]]	+	== Allosteric Inhibition of Caspase-7 ==
		+	It has been shown that caspases -3 and -7 can be inhibited at a site other than the active site by allosteric inhibitors, such as 5-Fluoro-1H-indole-2-carboxylic acid (2-mercapto-ethyl)-amide ('''FICA''') or 2-(2,4-Dichlorophenoxy)-N-(2-mercapto-ethyl)-acetamide ('''DICA'''), at the dimer-interface cavity. These inhibitors inactivate the enzyme on three different levels by: a) locking the L2' in a down conformation preventing it from ordering the active site loop bundles, b) rearranging the active site dyad H144 and C186, thereby affecting the ability to perform its chemistry, c) a conformational shift of residue R187, blocking substrate binding.

-	==~~Additional Resources~~==	+	<scene name='56/566502/Dica_bound_caspase_7/2'>Caspase-7 bound to allosteric inhibitor DICA</scene> at the dimer interface. The mechanism of allosteric inhibition of DICA starts with binding to C290 within the dimer interface, this displaces Y223. The movement of tyrosine from the partially active state of the enzyme forces R187 into a position that both physically blocks substrate binding, as well as, move the active site cysteine 186. The resulting conformational changes inactivate the enzyme, making it unable to process substrate.
-	~~For additional information, see: [[Cancer]]~~	+
-	<br />	+
		+	== Caspase-7 Dynamics ==
		+
		+
		+	Observed here is the <scene name='Molecular_Playground/Caspase_Dynamics/Morph2/2'>conformational change between substrate bound and substrate incompatible forms</scene> of Caspase-7. These dynamics show the dramatic conformational change of the cleaved semi-ordered protease upon binding to the substrate mimic DEVD-CHO. Substrate binding triggers rearrangement of the partially ordered loop bundles and the L2' loop. The newly assumed state stabilizes the protein.
		+
		+
		+	== References ==
		+
		+	Hardy, J. A., J. Lam, et al. (2004). "Discovery of an allosteric site in the caspases." Proc Natl Acad Sci U S A 101(34): 12461-12466.
		+
		+	Witkowski, W. a, & Hardy, J. a. (2009). L2’ loop is critical for caspase-7 active site formation. Protein science : a publication of the Protein Society, 18(7), 1459–68. doi:10.1002/pro.151
		+
		+	Witkowski, W. a, & Hardy, J. a. (2011). A designed redox-controlled caspase. Protein science : a publication of the Protein Society, 20(8), 1421–31. doi:10.1002/pro.673

Michal Harel at 08:05, 24 July 2011

2011-07-24T08:05:21Z

←Older revision		Revision as of 08:05, 24 July 2011
Line 17:		Line 17:

	'''Molecular Playground banner:''' Conformational Dynamics between active and allosterically inhibited caspase-7 elucidate the mechanism of allostery in this important class of cysteine proteases.		'''Molecular Playground banner:''' Conformational Dynamics between active and allosterically inhibited caspase-7 elucidate the mechanism of allostery in this important class of cysteine proteases.
		+
		+	==3D structures of caspase==
		+
		+	[[Caspase]]

	==Additional Resources==		==Additional Resources==
	For additional information, see: [[Cancer]]		For additional information, see: [[Cancer]]
	<br />		<br />

David Canner at 10:37, 1 October 2010

2010-10-01T10:37:59Z

←Older revision		Revision as of 10:37, 1 October 2010
Line 17:		Line 17:

	'''Molecular Playground banner:''' Conformational Dynamics between active and allosterically inhibited caspase-7 elucidate the mechanism of allostery in this important class of cysteine proteases.		'''Molecular Playground banner:''' Conformational Dynamics between active and allosterically inhibited caspase-7 elucidate the mechanism of allostery in this important class of cysteine proteases.
		+
		+	==Additional Resources==
		+	For additional information, see: [[Cancer]]
		+	<br />

Daniel Seeman at 14:18, 12 May 2010

2010-05-12T14:18:45Z

←Older revision		Revision as of 14:18, 12 May 2010
Line 17:		Line 17:

	'''Molecular Playground banner:''' Conformational Dynamics between active and allosterically inhibited caspase-7 elucidate the mechanism of allostery in this important class of cysteine proteases.		'''Molecular Playground banner:''' Conformational Dynamics between active and allosterically inhibited caspase-7 elucidate the mechanism of allostery in this important class of cysteine proteases.
-
-
-	=== (<span class="plainlinks">[http://www.proteopedia.org/wiki/index.php?title=Molecular_Playground/Caspases&action=edit&section=4 '''Expand CBI Entry for Caspases (click to edit)''' ]</span>) ===
-	::(<span class="plainlinks">[http://www.proteopedia.org/wiki/index.php?title=Molecular_Playground/Caspases&action=edit&section=4 '''Expand CBI Entry for Caspases (click to edit)''' ]</span>)

Daniel Seeman: Molecular Playground/Caspases moved to Molecular Playground/Caspase-7 Dynamics

2010-05-04T19:19:36Z

Molecular Playground/Caspases moved to Molecular Playground/Caspase-7 Dynamics

←Older revision

Revision as of 19:19, 4 May 2010

Daniel Seeman at 18:15, 4 May 2010

2010-05-04T18:15:10Z

←Older revision		Revision as of 18:15, 4 May 2010
Line 19:		Line 19:


		+	=== (<span class="plainlinks">[http://www.proteopedia.org/wiki/index.php?title=Molecular_Playground/Caspases&action=edit&section=4 '''Expand CBI Entry for Caspases (click to edit)''' ]</span>) ===
	::(<span class="plainlinks">[http://www.proteopedia.org/wiki/index.php?title=Molecular_Playground/Caspases&action=edit&section=4 '''Expand CBI Entry for Caspases (click to edit)''' ]</span>)		::(<span class="plainlinks">[http://www.proteopedia.org/wiki/index.php?title=Molecular_Playground/Caspases&action=edit&section=4 '''Expand CBI Entry for Caspases (click to edit)''' ]</span>)

Daniel Seeman at 18:14, 4 May 2010

2010-05-04T18:14:42Z

←Older revision		Revision as of 18:14, 4 May 2010
Line 19:		Line 19:


-	::(<span class="plainlinks>[http://www.proteopedia.org/wiki/index.php?title=Molecular_Playground/Caspases&action=edit&section=4 '''Expand CBI Entry for Caspases (click to edit)''' ]</span>)	+	::(<span class="plainlinks">[http://www.proteopedia.org/wiki/index.php?title=Molecular_Playground/Caspases&action=edit&section=4 '''Expand CBI Entry for Caspases (click to edit)''' ]</span>)

Daniel Seeman at 18:14, 4 May 2010

2010-05-04T18:14:24Z

←Older revision		Revision as of 18:14, 4 May 2010
Line 19:		Line 19:


-	::(<span class="plainlinks>[http://www.proteopedia.org/wiki/index.php?title=Molecular_Playground/Caspases&action=edit&section=4 '''Expand CBI Entry for Caspases (click to edit)''' ])</span>	+	::(<span class="plainlinks>[http://www.proteopedia.org/wiki/index.php?title=Molecular_Playground/Caspases&action=edit&section=4 '''Expand CBI Entry for Caspases (click to edit)''' ]</span>)

Daniel Seeman at 18:13, 4 May 2010

2010-05-04T18:13:56Z

←Older revision		Revision as of 18:13, 4 May 2010
Line 19:		Line 19:


-	*<span class="plainlinks>[http://www.proteopedia.org/wiki/index.php?title=Molecular_Playground/Caspases&action=edit&section=4 '''Expand CBI Entry for Caspases (click to edit)''' ]</span>	+	::(<span class="plainlinks>[http://www.proteopedia.org/wiki/index.php?title=Molecular_Playground/Caspases&action=edit&section=4 '''Expand CBI Entry for Caspases (click to edit)''' ])</span>